This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Percolator post-processes the results of a shotgun proteomics database search program, re-ranking peptide-spectrum matches so that the top of the list is enriched for correct matches. Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra. qvality performs nonparametric estimation of posterior error probabilities.